feat: enable output of unmapped reads (#1549)

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### Description

Ability to save unmapped reads in fastq or fastq.gz formats using the
`--outReadsUnmapped Fastx` option in STAR

### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/star/align/meta.yaml

@@ -5,6 +5,7 @@ authors:
   - Johannes Köster
   - Tomás Di Domenico
   - Filipe G. Vieira
+  - Kashyap Chhatbar
 notes: |
   * The `extra` param allows for additional program arguments.
   * It is advisable to consider updating the limits setting before running STAR,

bio/star/align/test/Snakefile

@@ -12,6 +12,7 @@ rule star_pe_multi:
         aln="star/pe/{sample}/pe_aligned.sam",
         log="logs/pe/{sample}/Log.out",
         sj="star/pe/{sample}/SJ.out.tab",
+        unmapped=["star/pe/{sample}/unmapped.1.fastq.gz","star/pe/{sample}/unmapped.2.fastq.gz"],
     log:
         "logs/pe/{sample}.log",
     params:
@@ -32,6 +33,7 @@ rule star_se:
         aln="star/se/{sample}/se_aligned.bam",
         log="logs/se/{sample}/Log.out",
         log_final="logs/se/{sample}/Log.final.out",
+        unmapped="star/se/{sample}/unmapped.fastq",
     log:
         "logs/se/{sample}.log",
     params:

bio/star/align/wrapper.py

@@ -42,6 +42,9 @@
 else:
     readcmd = ""
 
+out_unmapped = snakemake.output.get("unmapped", "")
+if out_unmapped:
+    out_unmapped = "--outReadsUnmapped Fastx"
 
 index = snakemake.input.get("idx")
 if not index:
@@ -64,6 +67,7 @@
         " --readFilesIn {input_str}"
         " {readcmd}"
         " {extra}"
+        " {out_unmapped}"
         " --outTmpDir {tmpdir}/STARtmp"
         " --outFileNamePrefix {tmpdir}/"
         " --outStd {stdout}"
@@ -83,3 +87,12 @@
         shell("cat {tmpdir}/Log.progress.out > {snakemake.output.log_progress:q}")
     if snakemake.output.get("log_final"):
         shell("cat {tmpdir}/Log.final.out > {snakemake.output.log_final:q}")
+    unmapped = snakemake.output.get("unmapped")
+    if unmapped:
+        # SE
+        if not fq2:
+            unmapped = [unmapped]
+
+        for i, out_unmapped in enumerate(unmapped, 1):
+            cmd = "gzip -c" if out_unmapped.endswith("gz") else "cat"
+            shell("{cmd} {tmpdir}/Unmapped.out.mate{i} > {out_unmapped}")